Contacts of the strand formed by residues 125 - 131 (chain E) in PDB entry 2Q5E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 125 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E VAL* 4.9 1.1 - - + -
123E ALA* 3.5 2.8 - - - +
124E ASP* 1.3 92.7 - - + +
126E ILE* 1.3 68.0 + - - +
127E VAL* 4.3 6.1 - - + -
138E VAL 4.2 0.2 - - - -
140E VAL* 2.7 61.3 + - + +
142E LYS* 3.3 44.0 - - + -
173E VAL* 5.0 5.6 - - + -
176E LEU* 3.6 62.6 - - + -
177E LEU* 4.1 15.9 - - + -
179E ARG* 5.5 2.5 - - - -
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Residues in contact with ILE 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ILE 5.2 2.2 - - - +
123E ALA* 4.1 11.0 - - + +
125E PHE* 1.3 80.8 - - - +
127E VAL* 1.3 66.6 + - - +
128E PRO* 4.0 5.0 - - - +
137E GLN* 3.6 33.7 - - + +
138E VAL 3.0 9.0 - - - +
139E TYR* 3.6 31.2 - - + -
176E LEU* 5.2 2.8 - - - +
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Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E PHE* 4.3 9.0 - - + -
126E ILE* 1.3 80.4 - - - +
128E PRO* 1.3 65.5 - - + +
129E ILE* 3.3 26.4 + - + -
137E GLN* 4.1 1.8 - - - -
138E VAL* 2.7 47.2 + - + +
140E VAL* 4.8 2.0 - - + -
172E PRO* 4.2 17.3 - - + +
173E VAL* 4.0 29.6 - - + -
176E LEU* 3.9 26.7 - - + -
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Residues in contact with PRO 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ILE 4.0 4.9 - - - +
127E VAL* 1.3 86.4 - - + +
129E ILE* 1.3 65.5 + - - +
135E THR* 4.9 10.8 - - + +
136E HIS 3.4 7.4 - - - +
137E GLN* 3.6 23.5 - - - +
172E PRO* 5.6 2.5 - - + +
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E VAL* 3.3 22.4 - - + -
128E PRO* 1.3 80.4 - - - +
130E GLU* 1.3 64.5 + - - +
131E ILE* 3.6 29.2 + - + -
134E THR 3.5 0.5 - - - +
135E THR* 3.1 5.9 - - - -
136E HIS* 2.8 37.0 + - + +
138E VAL* 3.2 31.2 - - + -
168E LYS* 4.0 29.2 - - + +
169E TYR* 3.7 27.1 - - + -
172E PRO* 5.1 0.7 - - + -
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ILE* 1.3 73.6 - - - +
131E ILE* 1.3 65.9 + - - +
132E GLU 4.1 1.1 + - - -
133E GLY* 3.3 32.8 + - - +
134E THR 3.5 5.6 - - - +
135E THR* 4.0 21.3 - - + +
168E LYS* 3.5 20.6 + - - +
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E PHE* 4.2 28.9 - - + -
129E ILE* 3.6 23.5 + - + -
130E GLU* 1.3 78.8 - - - +
132E GLU* 1.3 85.3 + - + +
134E THR* 2.7 28.0 + - - +
136E HIS* 3.8 22.3 + - + +
168E LYS* 4.2 14.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il